Obama in Indonesia: Will the President Speak Out on Human Rights?

US President Barack Obama speaks following a signing ceremony between Boeing and Indonesia's Lion Air on the sidelines of the Association of Southeast Asian Nations (ASEAN) and East Asia summits in Nusa Dua on Indonesia's resort island of Bali, on November 18, 2011. (Photo: Saul Loeb / AFP / Getty Images)

Obama loves Indonesia. He lived there as a boy and returned, last year, as president of the United States. In his homecoming speech at the University of Indonesia he reminisced about the Jakarta of his youth, conjuring scenes of rice paddies and kites drifting on the breeze. “Indonesia is a part of me,” he mused, lauding the young democracy for its tolerance and diversity. His affection for his onetime home is understandable. But, at this weekend’s East Asia Summit on Bali, he should hold the country to account for failing to live up to its purported ideals.

As I argued in an essay for this week’s magazine, the religious pluralism Obama praised last year is presently under threat:

In the past year, public violence against religious minorities, who together make up about 12% of the 240 million population, has been relentless: there has been a slew of incidents, from burnings and bombings of churches to attacks by radical Muslims on moderates. The authorities appear unable or unwilling to firmly intervene.

That seemed to be the case when I was in a packed courtroom outside Jakarta a few months ago. On trial were 12 men charged in connection with a mass assault early this year on members of the peaceful Ahmadiyah sect. Ahmadis believe that their Indian founder Mirza Ghulam Ahmad (1835-1908) was also a prophet, after Muhammad — a claim orthodox Muslims find heretical. This plus other differences have made Ahmadis a target for hard-liners in Pakistan, Bangladesh and, of late, Indonesia too. The attack on the Ahmadis was brutal. A hundreds-strong crowd gathered at opposite ends of a remote rice-farming village on the western edge of Java and converged on an Ahmadi home. The people inside were surrounded and attacked with machetes, sharpened sticks and stones. Three men died; five were badly injured.

At the trial, before the judges entered the chamber, an Islamic cleric in a white robe stepped from the gallery and led the courtroom in prayer. Those inside — plus many more pressed against the outside gate — prayed for the mob, not those killed. People in the crowd told me the Ahmadis had it coming, that the mob was provoked and the violence spontaneous.

One of the accused, 17-year-old Dani bin Misra, was filmed smashing an Ahmadi man’s skull with a rock. He and the other defendants were convicted of “participation in a violent attack that results in casualties.” Dani was sentenced to three months’ jail. The rest, including two clerics, received five to six months. (By contrast, an Ahmadi got six months for wounding an attacker when defending a family’s property.) Said New York City — based Human Rights Watch: “The trial sends the chilling message that attacks on minorities will be treated lightly by the legal system.” (Read the full piece here.)

Indonesia’s fledgling democracy is also being tested by events Papua. The western part of the island of New Guinea was once a Dutch colony, but has been Indonesian territory since a highly contested 1969 plebiscite known as the “Act of Free Choice.” Large segments of the indigenous Melanesian population oppose Indonesian rule and many want greater autonomy, or even full independence for the region. Indonesia opposes the movement and has repeatedly used force to quell secessionist sentiment.

On Oct. 17, Indonesia police and military forces attacked a peaceful protest in the city of Jayapura, killing three, arresting about 300 and injuring at least 96. New York-based Human Rights Watch is calling for an independent investigation into the incident. “Papuans peacefully calling for independence does not justify a deadly crackdown,” said deputy Asia director Elaine Pearson in a statement. “President Yudhoyono has an opportunity to show Papuans that he’s concerned about their rights by seriously investigating these deaths.” Obama also has an opportunity. He can tell Yudhoyono’s government that the world expects better from Indonesia. And that he does too.

Emily Rauhala is an Associate Editor at TIME. Find her on Twitter at @emilyrauhala. You can also continue the discussion on TIME’s Facebook page and on Twitter at @TIME.